June 27, 2013

The Maikop cranium from Mandzhikiny I in Kalmykia was
measured by A.A. Khokhlov. In his view, it resembles the previously published
Maikop and Novosvobodnaya specimens. Khokhlov pointed to certain features common
to the Maikop and Novosvobodnaya people and opposing them to the Pit Grave
people. He questioned the resemblance between the Maikop crania from Evdyk I and
those from Syezzheye and Zadono-Avilovsky; and he believed the former to
resemble crania from the Caucasus, the Near East, and Southwestern Central
Asia, being closest to those from Samtavro, Georgia, and Ginchi, Dagestan
(Khokhlov, 2002).

In a brief note, M.M Gerasimova, D.V. Pezhemsky, and L.T.
Yablonsky (2002) described several Maikop crania from burial grounds on the
Kalaus River in the Stavropol Region. The series is diverse and, judging by the
results of multivariate analysis, is closest to the Chalcolithic group from
Khvalynsk in the Samara Region.

T.I. Alekseyeva (2004) measured a male skull from mound 13
burial 5 at Nezhinskaya near Kislovodsk (the plastic reconstruction of this
individual’s appearance was made by L.T. Yablonsky), as well as two crania
(male and female) from mound 70 burial 1 at Zamankul in Northern Ossetia. All
these crania came from “Maikop– Novosvobodnaya” burials and were attributed to
the Mediterranean variety of the Southern Caucasoid type which was distributed
in Armenia, Georgia, Iran, and Mesopotamia during the Chalcolithic and Early Bronze
Age. The heterogeneity of the Maikop group in Alexeyeva’s opinion may be due to
individual variability, but also to admixture with the natives of the
southeastern European steppes (Alekseyeva, 2004).

Later, Gerasimova, Pezhemsky, and Yablonsky (2007) published
a large article where crania from burial grounds on the Kalaus River were
described in detail. They noted that the Maikop series is heterogeneous but on
average it represented the Eastern Mediterranean trait combination. The latter
is quite dissimilar to the Cromagnoid combination typical of certain Bronze Age
groups of the Eastern European steppes. The idea that at least some Maikop
people were descendants of immigrants from the Near East was deemed probable;
however the role of the steppe admixture, possibly accounting for a somewhat
greater robustness of Maikop crania compared to Mediterranean ones, was not
excluded either.

And the author's own conclusions:

In sum, the results of the multivariate analysis suggest that
Maikop people are distinct from all the contemporary and later Eastern European
groups of the steppe and forest-steppe zones. This provides an additional
argument in favor of the hypothesis that Maikop burials in Kalmykia attest not
merely to the cultural impact of the Maikop community on the steppe tribes
(Munchaev, 1994: 168); rather, they were left by a separate group which was unrelated
to the local Pit Grave population by origin. The Southern Caucasoid trait
combination revealed by the Maikop series is somewhat similar to that shown by
the contemporaneous groups of the Northern Caucasus and southern Turkmenia.
Clearly, this does not imply a direct connection with any of these regions.

The Near Eastern parallels are no less suggestive (Bunak,
1947: 77). Thus, a small series from Al-Ubaid in southern Mesopotamia, dating
from the 4th millennium BC, is characterized by dolichocrany (cranial index, 72.6),
a high face, medium wide, high and sharply protruding nose, and wide palate
(Keith, 1931: 239–241). Regrettably, the number of measurements is too small to
warrant a reliable comparison with the Maikop series. However, the isolated
position of the Maikop group in Eastern Europe, its vague resemblance to the
Southern Caucasoids of the Caucasus and Southwestern Central Asia, and the Near
Eastern cultural affinities of Maikop and Novosvobodnaya (Munchaev, 1994: 170)
indirectly point to Near Eastern provenance.

It would certainly be interesting to obtain DNA from some of these specimens.

Abstract
Measurements of crania of people associated with the Early Bronze Age Maikop culture of the Northern Caucasus are analyzed. Data on Maikop males, new and previously published, were compared with those concerning chronologically and geographically related people using the canonical variate analysis. The Maikop series turned out to be isolated and no close parallels to it were found among the Bronze Age groups, either from the steppe and forest-steppe zones of Eastern Europe or from the Caucasus and Southwestern Central Asia. While certain parallels seem to point to the Near East, they are too few to warrant definite conclusions.

June 26, 2013

Elastic energy storage in the shoulder and the evolution of high-speed throwing in Homo

Neil T. Roach et al.

Some primates, including chimpanzees, throw objects occasionally1, 2, but only humans regularly throw projectiles with high speed and accuracy. Darwin noted that the unique throwing abilities of humans, which were made possible when bipedalism emancipated the arms, enabled foragers to hunt effectively using projectiles3. However, there has been little consideration of the evolution of throwing in the years since Darwin made his observations, in part because of a lack of evidence of when, how and why hominins evolved the ability to generate high-speed throws4, 5, 6, 7, 8. Here we use experimental studies of humans throwing projectiles to show that our throwing capabilities largely result from several derived anatomical features that enable elastic energy storage and release at the shoulder. These features first appear together approximately 2 million years ago in the species Homo erectus. Taking into consideration archaeological evidence suggesting that hunting activity intensified around this time9, we conclude that selection for throwing as a means to hunt probably had an important role in the evolution of the genus Homo.

It is nothing short of a world record in DNA research that scientists at the Centre for GeoGenetics at the Natural History Museum of Denmark (University of Copenhagen) have hit. They have sequenced the so far oldest genome from a prehistoric creature. They have done so by sequencing and analyzing short pieces of DNA molecules preserved in bone-remnants from a horse that had been kept frozen for the last 700.000 years in the permafrost of Yukon, Canada. By tracking the genomic changes that transformed prehistoric wild horses into domestic breeds, the researchers have revealed the genetic make-up of modern horses with unprecedented details. The spectacular results are now published in the international scientific journal Nature.

...

First, by comparing the genome in the 700,000 year old horse with the genome of a 43,000 year old horse, six present day horses and the donkey the researchers could estimate how fast mutations accumulate through time and calibrate a genome-wide mutation rate. This revealed that the last common ancestor of all modern equids was living about 4.0-4.5 million years ago. Therefore, the evolutionary radiation underlying the origin of horses, donkeys and zebras reaches back in time twice as long as previously thought. Additionally, this new clock revealed multiple episodes of severe demographic fluctuation in horse history, in phase with major climatic changes such as the Last Glacial Maximum, some 20,000 years ago.

I'll add the paper abstract later.

Nature (2013) doi:10.1038/nature12323

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

Ludovic Orlando et al.

The rich fossil record of equids has made them a model for evolutionary processes1. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560–780 thousand years before present (kyr BP)2, 3. Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43?kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski’s horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0–4.5?million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus4, 5. We also find that horse population size fluctuated multiple times over the past 2?Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski’s and domestic horse populations diverged 38–72?kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski’s horse investigated. This supports the contention that Przewalski’s horses represent the last surviving wild horse population6. We find similar levels of genetic variation among Przewalski’s and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski’s horse. Such regions could correspond to loci selected early during domestication.

June 25, 2013

An extensive English summary of an article in Russian by Gamkrelidze and Ivanov almost 30 years since the publication of their original book. There are other articles in the volume of the JOLR presenting different views (unfortunately most behind a paywall).

Indo-European homeland and migrations: half a century of studies and discussions [In Russian with English summary]

The problem of the initial place from which the original Indo- European dialects spread over Eurasia has been studied by several generations of scholars. Few alternative points of view have been proposed: first an area near the North Sea (in the works of some scholars of the border of the 19th and 20th centuries), then the North coast of the Black Sea (an old idea of Schrader revived by Maria Gimbutas and her followers) or an area closer to the more eastern (Volga-Ural) parts of Central Eurasia. 40 years ago we suggested first in a talk at a conference, then in a series of articles and in a resulting book (published in Russian in 1984) that the Northern part of the Near East (an area close to North-East Syria and North Mesopotamia) may be considered as a possible candidate for the Indo-European homeland; similar suggestions were made by C. Renfrew and other scholars in their later works. Recent research on these topics has brought up additional evidence that seems to prove the Near Eastern hypothesis for the time that had immediately preceded the dispersal of the Indo-European protolanguage. Indirect evidence on the early presence of Indo-Europeans in the areas close to the Near East can be found in the traces of ancient contacts between linguistic families in this part of Eurasia. Such contacts between Proto-Indo-European and Proto-Kartvelian have been suggested in the work of T. Gamkrelidze and G. Mach’avariani more than 60 years ago. The following studies have established a number of important loanwords from Proto-Indo-European in Proto-Kartvelian. Particularly interesting discoveries in this field were made by the late G. A. Klimov. He has found many new common elements of the two families in addition to a relatively long list in our joint work. The main difficulty in interpreting the results of his investigations is connected to the problem of a possible common Nostratic origin both of Proto-Indo-European and of Proto-Kartvelian. If these two linguistic families were originally cognate, then some part of the correspondences found by Klimov and other scholars might be traced back to the early period of Proto-Nostratic (more than 10 000 years ago). Only those words that were not inherited from this ancient time are important as a proof of the later presence of Proto-Indo-European in the area close to the Proto-Kartvelian (to the southwest of the Transcaucasian area in which the latter spread in the historic time). In our book, published in 1984, we suggested some common terms shared by these languages, explaining them as possible traces of later Indo-European (probably Indo-Iranian) migrations through the Caucasus. The study of this problem has been enriched through the recent research on Proto-North Caucasian. S. L. Nikolaev and S. A. Starostin have compiled a large etymological dictionary of this family, furthering the comparative studies started by Prince N. S. Trubetzkoy. Starostin has gathered a large collection of the terms of material culture common to North Caucasian and Indo-European. They include many names of domestic animals and animal body parts or products of cattle-breeding, plants and implements. In a special work on this subject Starostin suggested that all these terms were borrowed in the area of the Near East to the South of Transcaucasia in the early 5th mil. BC. Although we still use the traditional term “North Caucasian”, it is not geographically correct even if applied to such living languages as Abkhaz and to the extinct Ubykh (spoken originally at the southern part of the South-West Transcaucasian area). Since both Hurro-Urartian and Hattic (two ancient dialects of this linguistic group) were spoken in the regions to the South of Transcaucasia already in the 3rd mil. BC, it becomes possible to pinpoint the homeland of the whole family (which at that time was not North Caucasian) in the same area close to the supposed Proto-Indo-European and Proto-Kartvelian homelands. The fricative š in the Hurrian name for ‘horse’, eššə, and an affricate *č (> š) in the forms of the other North Caucasian dialects correspond to the Proto-Indo-European palatal stop *k’ that has become an affricate *č and then a fricative š /s in the Indo-European languages of the satəm type. Similar changes are present in the other borrowings discussed by Starostin. He supposed that the common words discovered by him were mostly borrowed from Proto-North Caucasian (or from a dialect of it) into Proto-Indo-European. The opposite direction of borrowing from an Indo-European dialect of a satəm type can be suggested due to the typologically valid laws of sound change. But no matter which direction of the borrowing should be chosen, the existence of these loanwords is beyond doubt. They clearly point to the location of the Indo-European homeland. In our monograph we suggested that several words shared by Semitic and Indo-European (such as the ancient term for ‘wine’, Hittite wiyana­) can be considered Proto-Indo-European borrowings (as distinct from the rest of the most ancient old Semitic or Afro-Asiatic loanwords in Proto-Indo-European). S. A. Starostin suggested that a large number of (mainly West) Semitic words that did not have correspondences in the other Afro-Asiatic languages had been borrowed from Proto-Indo-European. He came to the conclusion: “the original Indo-European (Indo-Hittite) homeland was somewhere to the North of the Fertile Crescent from where the descendents of Indo-Hittites could have moved in two directions (starting with early 5th millennium BC) to the South where they came into the contact with the Semites, and indeed could have driven a part of them further to the South, and to the North (North-East) whence they ultimately spread both to Europe and to India”. The interference of the early dialects of Proto-Indo-European, Proto-Semitic and Proto-Kartvelian to which the early Proto-“North” Caucasian can be added might have led to the formation of a sort of linguistic zone (Sprachbund) that not only shared many words pertaining to a new farming economy, but also had several phonological and grammatical features in common. After we had published our hypothesis on the Near Eastern homeland of the Indo-Europeans, several scholars asked us why, at a time when writing had already been invented, there were no written documents testifying to the presence of Indo-Europeans in these areas. It seems that now there are several possible answers to the question. The great specialist on Iranian, W. B. Henning, who had worked for many years on the problem of the name of Tocharians, suggested in a posthumous article that their early ancestors were Gutians who had invaded Mesopotamia in ca. 2350—2200 BC. In an article written after we had already published our book, we have developed Henning’s idea (based mainly on the etymological links of Near Eastern Guti and Tukri and Central Asian names of corresponding Indo-European Kuchean and Tocharian ethnic groups), also paying attention to the possible explanation of some names of Gutian kings preserved in Sumerian texts. Recently it has been suggested that an unknown “Pre-Sumerian” language, reconstructed on the basis of the phonetic values of many cuneiform signs, was an archaic “Euphratic” Indo-European dialect spoken in Southern Mesopotamia in the second half of the 4th mil. BC. According to this hypothesis, the phonetic values of approximately one hundred of the early signs that are different from the Sumerian ones go back to the Euphratic words. A large number of Anatolian personal names (of a very archaic Indo-European type) have been found in the Old Assyrian texts from trade colonies in Asia Minor. The continuation of the excavations in Kanish that have yielded more than 23000 cuneiform tablets has made it possible to discover in them many Anatolian Indo-European names and loanwords. The Old Assyrian documents in Kanish are encountered in the archaeological levels II and Ib dated by the first centuries of the 2nd mil. BC (on the base of the recently found lists of eponyms); they precede Old Hittite texts for ca. 250 years. At that time the two Anatolian groups of dialects — a Northern (Hittite) one, displaying centum dialect features, and a Southern (Luwian), partly similar to the satəm languages — were already quite distinct. From the very beginning, the idea of the Indo-European homeland in the Near East was connected to the discovery of a possible link between the appearance of speakers of Indo-European dialects in Europe and the spread of the new farming technology. This trend of thought has been developed in the archeological works of Sir Colin Renfrew. Subsequent attempts to support this hypothetical connection were made by comparing genetic data on the time and space characteristics of the European population. The farming terms common to Indo-European and other linguistic families discussed above show that the innovations were not restricted to one group of languages and were transmitted and exchanged between different ethnic formations. The area of the interference of these families coincides with the kernel of the rising farming in the Near East. That process of global (multilingual and multicultural) change had led to the diffusion of the results of the Neolithic revolution. The main directions of this diffusion coincide with the trends of the Indo-European migrations, but the new objects might have been introduced earlier than some of their Indo-European names and the latter might precede the coming of those who coined the terms. The spread of Near Eastern innovations in Europe roughly coincides with the split of Proto-Indo-European (possibly in the early 5th mil. BC), but some elements of the new technology and economy might have penetrated it much earlier (partly through the farmers close to the Tyrrhenian population as represented 5300 years ago by the genome of the Tyrolean Iceman). The diffusion took several thousand years and was probably already all over Europe ca. 3550 BC. At that time Indo-European migrations were only beginning. The speakers of the dialects of Proto-Indo-European living near the kernel of the technological revolution in Anatolia should have acquired the main results of this development. The growth of farming economy in Europe became more active with the split of the proto-language and the dispersal of the Indo-Europeans. The astonishing scope and speed of that process were afforded by the use of the domesticated horse and wheeled vehicles. The Indo-Europeans did not have to be pioneers in this field, but they were probably skillful in spreading other peoples’ innovations. Recent work on the Botai culture of North Kazakhstan makes it possible to suppose a contribution of the Proto-Yeniseian people to the development of horse domestication. For approximately fifteen hundred years serious preparatory work on horse domestication and the use of wheeled vehicles had been going on in different parts of Eurasia. Then, almost suddenly, the results are witnessed. On the border of the 3rd and 2nd mil. BC both of these important innovations appear together, usually in a context implying the presence of Indo-Europeans: traces of Near East-type chariots and the ritual use of the horse are clear in (probably Ancient Iranian) Margiana (Gonur), we see chariots on the Anatolian type of seals in Kanish; Hurrian sculptures and other symbols of horse abound in Urkeš as if foretelling the future Mespotamian-Aryan and Hurrian excellent training of horses in Mitanni (as later in Urartu). One of the first examples of the sacrificial horses used together with chariots in an archaic ritual was found in Sintashta; the following studies of the cities of the Transuralian Sintashta-Arkaim area made it clear that some Indo-European (and maybe Iranian as well) elements were at least partly present there. The movement of Indo-Europeans to the north of the Caspian Sea in the northeast direction documented in the Sintashta-Arkaim complex led them much farther to the Altai-Sayany area where recent genetic investigations found traces of a Caucasoid element. Another Indo-European group moving in a parallel eastward direction using the South Silk Road caused the presence of a similar anthropological group among the population of Central Asia. It may be supposed that the Caucasoid anthropological type of the Iranian and/or Tocharian population of Eastern Turkestan, attested in the mummies recently found there as well as in the contemporary images of the native people, should be considered as the result of these migrations from the West to the East. The problem whether the boats played a role comparable to that of chariots at the time of early migrations is still to be decided by maritime archaeology. It seems that before the efficient use of chariots and horses, long-term mass movements were hardly possible. The first changes in the geographical position of separate dialects, e.g. when the Anatolians separated the Greeks from the rest of the East Indo-European group (that included the Armenians and Indo-Iranians), were caused by rather small-scale migrations close to the original homeland in the Near East.

[The first part of the project looked for copper and Bronze Age cultures of the steppe west and north of the Black Sea (Fig. 1). In the Late Bronze Age (around 3000 BC) came here the very mobile Yamnaya culture in appearance, their population and influence radius - as the investigations showed - apparently at the same time expanding consolidated. With the Yamnaya culture is a single burial rites used in so-called pit graves under kurgans (grave mound). Also this wont Halbno addition maggots strong trading relationships across the steppe. Around 2500 BC, they were replaced by the less mobile Katakombengrab-culture whose dissemination conduction region was significantly smaller.Population genetic analyzes of DNA occupied by the late copper to the Middle Bronze Age, a steadily increasing genetic distance between those cul tures. Between copper and time Katakombengrab culture is the genetic distance is greatest. Here the differences are much more pronounced than between early Chalcolithic cultures and Yamnaya population. This population genetic change could be an indication of discontinuity and population changes due to migration. An archaeological site of suspected immigration from eastern steppe areas but at least on the female side hardly taken place: For Central Asia typical DNA lines do not occur in the studied populations. Despite the genetic differences within the un the investigated groups are with them to popu lations, which are without doubt be described as European.Here the differences are much more pronounced than between early Chalcolithic cultures and Yamnaya population. This population genetic change could be an indication of discontinuity and population changes due to migration. An archaeological site of suspected immigration from eastern steppe areas but at least on the female side hardly taken place: For Central Asia typical DNA lines do not occur in the studied populations. Despite the genetic differences within the un the investigated groups are with them to popu lations, which are without doubt be described as European. DNA markers with known phenotype suggest a continuity between the North Pontic area of ​​4 / 3 Millennium BC and today's Europeans out. For instance, have all examined individuals tierungstyp on a bright pigments, as is prevalent in Europe today. Only the eye color has been dark in comparison to today.]

[The second part of the project was devoted to the population dynamics of early Iron Age peoples of nomadic horsemen in the Eurasian steppe belt. Here were 900-300 BC disseminated numerous highly mobile populations that are associated with the so-called Scythian or Sakian culture (Fig. 2). The groups studied are from the areas of eastern Kazakhstan, Altai mountains, Minusinsk Basin and Tuva. They all consist of a mixture of DNALinien, which today is a part of Central and East Asia and the other in Europe. Ity of the ground because this way the populations have a remarkably high level of genetic diversity that characterizes the Altai population today.

...

The Tagar Culture (Minusinsk Basin) this shows the greatest genetic - but also cultural - distance to all other groups. Although it chronologically corresponds to the Pazyryk culture of the Altai (5th-3rd century BC) seems to be present here genetic isolation. Between the Pazyryk culture and the significantly older findings from Tuva (7 / 6th century BC), however, the genetic distance in spite of the time interval is very small. Amazingly, has the Pazyryk culture also within its range a geographic substructure: Divided into Kazakh Altai, and Cuja Ukok plateau region, show the nomadic horsemen of Cuja region in relation to the other two groups increased genetic distance.]

June 21, 2013

The Maikop parallels with northern Mesopotamia or, more broadly, with the ancient Near East, and the seemingly consistent and growing number of calibrated radiocarbon determinations (currently more than 40 such dates; E. N. Chernykh personal communication) not only date the Maikop phenomenon more securely but also suggest some connections -albeit hard to specify- with larger historical processes, such as the north Mesopotamian, and later Uruk expansion into eastern Anatolia. The calibrated radiocarbon dates suggest that the Maikop culture seems to have had a formative influence on kurgan burial rituals and what now appears to be the later Pit-Grave (Yamnaya) culture on the Eurasian steppe (Chernykh and Orlovskaya 2004a: 97).

...

In other words, the fact that such a symbolic Mesopotamian practice is attested in the richest known "royal," or chiefly, Maikop burial must have significance not only for the earlier dating of the Maikop culture, but also for determining aspects of its cultural affiliation and formation.

Other scholars have focused on the northern steppe component of the Maikop culture. ... V. A. Trifonov (2004: 58-60) in a reappraisal and comparison of the so-called royal tomb at Arslantepe with the Novosvobodnaya-phase Maikop burials, reverses the arrow of cultural transmission and borrowing and argues for an eastern Anatolian Chalcolithic origin of the Novosvobodnaya tombs, such as documented at Korucutepe. Thus, if Trifonov is correct, and if the calibrated radiocarbon dates securely place Maikop chronologically before the emergence of the Pit-Grave (Yamnaya) horizon, then somewhat counterintuitively, the origins of raising large barrows or kurgans above the broad, flat expanse of the steppes may not have been indigenous but may have been derived from eastern Anatolia or the northern periphery of the greater ancient Near East.

...

It is probably futile to seek a single source from which the Maikop culture emerged.

Although the genetic heritage of the native populations of Sakha is mostly of East Asian ancestry, analyses of autosomal SNP data as well as haploid loci also show a minor West Eurasian genetic component. The patchy presence of the “European” (blue) component in the ADMIXTURE plot (Figure 6), most pronounced in Yukaghirs, probably testifies to recent admixture with Europeans. In addition, the presence of European-specific paternal lineages R1a-M458, I1 and I2a among Yakuts, Dolgans, Evenks and Yukaghirs likely points to a recent gene flow from East Europeans. Although only individuals with self-reported unadmixed ancestry for at least two generations were included in the study of haploid loci, mistakes in ethnic self-identification cannot be entirely excluded. One of the main sources of gene flow has likely been Russians who accounted for 37.8% of the population of Sakha in 2010 [61]. The migration of Russians (at first mainly men) to eastern Siberia started already in the 17th century, when Yakutia was incorporated into the Russian Empire [62].

But:

The mtDNA haplogroup J detected in the remains from a Yakut
burial site dated to the beginning of
the 17th century [41], long before the beginning of the settlement of Russian families in the 18th century [63], clearly
points to more ancient gene flow from western Eurasia. The presence of haplogroups H8, H20
and HV1a1a among the Yakuts, Dolgans and Evenks (Figure 1) also suggests gene flow
other than from Russians, because these haplogroups
are rare (H8 and H20) or even absent (HV1a1a) among Russians [64-67], but are common among southern Siberian populations as
well as in the Caucasus, the Middle and Near
East [19,68-70]. Moreover, the HVSI haplotypes of H8, H20a and HV1a1a in our sample exactly match those in the Buryats from
the Buryat Republic [19]. Similarly, the Ychromosome haplogroup J in Dolgans
and Evens very likely testifies to gene flow through South Siberia, as it is present among native
South Siberian populations [47,71]. The scenario of ancient gene flow from West Eurasia is
supported by ancient DNA data, which show that in the Bronze and Iron Ages, South Siberia,
including the Altai region, was an area of overwhelmingly predominant western Eurasian
settlement [72,73], and the Indo-European migration even reached northeastern Mongolia
[74]. To summarize, the West Eurasian genetic
component in Sakha may originate from recent admixture with East Europeans, whereas more ancient gene flow from West
Eurasia through Central Asia and South Siberia is also probable.

BMC Evolutionary Biology 2013, 13:127 doi:10.1186/1471-2148-13-127

Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia

Sardana A Fedorova et al.

Abstract (provisional)

Background

Sakha -- an area connecting South and Northeast Siberia -- is significant for understanding the history of peopling of Northeast Eurasia and the Americas. Previous studies have shown a genetic contiguity between Siberia and East Asia and the key role of South Siberia in the colonization of Siberia.

Results

We report the results of a high-resolution phylogenetic analysis of 701 mtDNAs and 318 Y chromosomes from five native populations of Sakha (Yakuts, Evenks, Evens, Yukaghirs and Dolgans) and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia. Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia. Analysis of autosomal SNP data confirms the genetic continuity between Sakha and South Siberia. Maternal lineages D5a2a2, C4a1c, C4a2, C5b1b and the Yakut-specific STR sub-clade of Y-chromosome haplogroup N1c can be linked to a migration of Yakut ancestors, while the paternal lineage C3c was most likely carried to Sakha by the expansion of the Tungusic people. MtDNA haplogroups Z1a1b and Z1a3, present in Yukaghirs, Evens and Dolgans, show traces of different and probably more ancient migration(s). Analysis of both haploid loci and autosomal SNP data revealed only minor genetic components shared between Sakha and the extreme Northeast Siberia. Although the major part of West Eurasian maternal and paternal lineages in Sakha could originate from recent admixture with East Europeans, mtDNA haplogroups H8, H20a and HV1a1a, as well as Y-chromosome haplogroup J, more probably reflect an ancient gene flow from West Eurasia through Central Asia and South Siberia.

Conclusions

Our high-resolution phylogenetic dissection of mtDNA and Y-chromosome haplogroups as well as analysis of autosomal SNP data suggests that Sakha was colonized by repeated expansions from South Siberia with minor gene flow from the Lower Amur/Southern Okhotsk region and/or Kamchatka. The minor West Eurasian component in Sakha attests to both recent and ongoing admixture with East Europeans and an ancient gene flow from West Eurasia.

I will simply note that the authors use the effective mutation rate that is ~1/3 the genealogical mutation rate and hence their age estimates are inflated by ~3x. I have expressed reservations about using Y-STR based age estimates in general, but these concerns become more important for older lineages.

In particular, I would be very surprised if Y-haplogroup N turns up in Europe 8-10 thousand years ago, and I expect to see it make its first appearance in the 3rd millennium BC or thereabouts, perhaps together with the Seima-Turbino expansion across northern Eurasia. Thanks to the ancient DNA -preserving boreal cold, it may be possible to find out.

Irrespective of my disagreement on the mutation rate issue, I have to applaud the comprehensive survey carried out by these Chinese scientists: numbers invariably pay off.

PLoS ONE 8(6): e66102. doi:10.1371/journal.pone.0066102

Genetic Evidence of an East Asian Origin and Paleolithic Northward Migration of Y-chromosome Haplogroup N

Hong Shi et al.

The Y-chromosome haplogroup N-M231 (Hg N) is distributed widely in eastern and central Asia, Siberia, as well as in eastern and northern Europe. Previous studies suggested a counterclockwise prehistoric migration of Hg N from eastern Asia to eastern and northern Europe. However, the root of this Y chromosome lineage and its detailed dispersal pattern across eastern Asia are still unclear. We analyzed haplogroup profiles and phylogeographic patterns of 1,570 Hg N individuals from 20,826 males in 359 populations across Eurasia. We first genotyped 6,371 males from 169 populations in China and Cambodia, and generated data of 360 Hg N individuals, and then combined published data on 1,210 Hg N individuals from Japanese, Southeast Asian, Siberian, European and Central Asian populations. The results showed that the sub-haplogroups of Hg N have a distinct geographical distribution. The highest Y-STR diversity of the ancestral Hg N sub-haplogroups was observed in the southern part of mainland East Asia, and further phylogeographic analyses supports an origin of Hg N in southern China. Combined with previous data, we propose that the early northward dispersal of Hg N started from southern China about 21 thousand years ago (kya), expanding into northern China 12–18 kya, and reaching further north to Siberia about 12–14 kya before a population expansion and westward migration into Central Asia and eastern/northern Europe around 8.0–10.0 kya. This northward migration of Hg N likewise coincides with retreating ice sheets after the Last Glacial Maximum (22–18 kya) in mainland East Asia.

June 20, 2013

We investigate the effect of spatial range expansions on the evolution of fitness when beneficial and deleterious mutations co-segregate. We perform individual-based simulations of a uniform linear habitat and complement them with analytical approximations for the evolution of mean fitness at the edge of the expansion. We find that deleterious mutations accumulate steadily on the wave front during range expansions, thus creating an expansion load. Reduced fitness due to the expansion load is not restricted to the wave front but occurs over a large proportion of newly colonized habitats. The expansion load can persist and represent a major fraction of the total mutation load thousands of generations after the expansion. Our results extend qualitatively and quantitatively to two-dimensional expansions. The phenomenon of expansion load may explain growing evidence that populations that have recently expanded, including humans, show an excess of deleterious mutations. To test the predictions of our model, we analyze patterns of neutral and non-neutral genetic diversity in humans and find an excellent fit between theory and data.

June 19, 2013

Reconstructing Native American Migrations from Whole-genome and Whole-exome Data

Simon Gravel et al.

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR.Native American ancestry in PUR appears most closely related to Equatorial-Tucanoan-speaking populations, supporting a Southern America ancestry of the Taino people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a three-population demographic model. The ancestral populations to the three groups likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features a Mexican population of 62,000, a Colombian population of 8,700, and a Puerto Rican population of 1,900. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest size and the earlier migration from Europe.

Objective—Haplogroup I of male-specific region of the human Y chromosome is associated with 50% increased risk of coronary artery disease. It is not clear to what extent conventional cardiovascular risk factors and genes of the male-specific region may explain this association.

Approach and Results—A total of 1988 biologically unrelated men from 4 white European populations were genotyped using 11 Y chromosome single nucleotide polymorphisms and classified into 13 most common European haplogroups. Approximately 75% to 93% of the haplotypic variation of the Y chromosome in all cohorts was attributable to I, R1a, and R1b1b2 lineages. None of traditional cardiovascular risk factors, including body mass index, blood pressures, lipids, glucose, C-reactive protein, creatinine, and insulin resistance, was associated with haplogroup I of the Y chromosome in the joint inverse variance meta-analysis. Fourteen of 15 ubiquitous single-copy genes of the male-specific region were expressed in human macrophages. When compared with men with other haplogroups, carriers of haplogroup I had ≈0.61- and 0.64-fold lower expression of ubiquitously transcribed tetratricopeptide repeat, Y-linked gene (UTY) and protein kinase, Y-linked, pseudogene (PRKY) in macrophages (P=0.0001 and P=0.002, respectively).

Conclusions—Coronary artery disease predisposing haplogroup I of the Y chromosome is associated with downregulation of UTY and PRKY genes in macrophages but not with conventional cardiovascular risk factors.

June 17, 2013

Interesting commentary by the author of a 1988 undergraduate thesis that revolved around re-measuring part of Morton's skulls and concluding (contra Gould) that Morton's measurements were accurate.

I haven't read it fully (it is in four parts), but here is the concluding paragraph from part 4:

In the final analysis, the Morton-Gould Affair, which has been popularized as a diagnostic example of the role of unconscious bias in science, is simply a case of two over-eager scholars jumping to conclusions based on a small amount of data. It is unfortunate that the discussion of Morton’s work has occupied so much energy over the past 30 years, when a more important issue is Gould’s historically inaccurate misrepresentation of Blumenbach’s work, which unlike Morton’s was a foundational element of modern physical anthropology and public policy regarding racial variation that still impacts us today. A proper representation of Blumenbach’s theories and an accurate translation of his major Latin publications into modern English and German are long overdue and would be of great benefit to science and society at large.

Should be interesting reading for anyone fascinated by the history of ideas.

June 14, 2013

My own half-baked idea is that because humans have longer childhoods and are very dependent on their mothers during their childhoods, there's an advantage to live past their reproductive years.

If a couple of women cease reproduction at 40 but one of them dies at 40 and the other at 50, there's a greater probability that the latter's offspring will survive and reproduce themselves.

So, increasing the gap between menopause and death increases the chances of success for offspring (because their mother lives longer to support them into adulthood). As childbirth becomes ever more dangerous (because of normal aging process) it "pays more" to stay alive and raise the kids already born than to gain more kids, at the risk of losing the ones you already have.

PLoS Comput Biol 9(6): e1003092. doi:10.1371/journal.pcbi.1003092

Mate Choice and the Origin of Menopause

Richard A. Morton et al.

Human menopause is an unsolved evolutionary puzzle, and relationships among the factors that produced it remain understood poorly. Classic theory, involving a one-sex (female) model of human demography, suggests that genes imparting deleterious effects on post-reproductive survival will accumulate. Thus, a ‘death barrier’ should emerge beyond the maximum age for female reproduction. Under this scenario, few women would experience menopause (decreased fertility with continued survival) because few would survive much longer than they reproduced. However, no death barrier is observed in human populations. Subsequent theoretical research has shown that two-sex models, including male fertility at older ages, avoid the death barrier. Here we use a stochastic, two-sex computational model implemented by computer simulation to show how male mating preference for younger females could lead to the accumulation of mutations deleterious to female fertility and thus produce a menopausal period. Our model requires neither the initial assumption of a decline in older female fertility nor the effects of inclusive fitness through which older, non-reproducing women assist in the reproductive efforts of younger women. Our model helps to explain why such effects, observed in many societies, may be insufficient factors in elucidating the origin of menopause.

Researchers have sourced William’s Indian ancestry to Eliza Kewark, his great-great-great-great-great grandmother, who was assumed to be Armenian, but now has been revealed as an Indian by genetic research.

...

“Through genealogy we traced two living direct descendants of Eliza and by reading the sequence of their mtDNA, we showed not only that they matched, but also that it belongs to a haplogroup called R30b, thus determining Eliza Kewark’s haplogroup,” the research team revealed.

The haplogroup, which is a group of related ancestral lineages, in this case was revealed to be rare and found only in South Asia. Other related branches of R30a and R30* are also entirely South Asian.

“This confirms therefore that the mtDNA of Eliza Kewark of Surat was of Indian heritage. R30b is rare even in India, where roughly 0.3 per cent of people carry this lineage,” the researchers revealed.

Personally, I wouldn't be so quick in discounting the traditional genealogical story. A lineage that occurs at a frequency of 0.3% will almost certainly be missed in any small sample if it occurs at similar trace frequencies in other populations.

June 12, 2013

Microsatellites may be a little "retro" in the age of million-SNP arrays and whole genome sequencing, but one has to admit that the following figure, resulting from a merge of multiple microsatellite datasets, is pretty impressive.

G3: Genes|Genomes|Genetics doi: 10.1534/g3.113.005728

Population Structure in a Comprehensive Genomic Data Set on Human Microsatellite Variation

Trevor J. Pemberton et al.

Over the past two decades, microsatellite genotypes have provided the data for landmark studies of human population-genetic variation. However, the various microsatellite data sets have been prepared with different procedures and sets of markers, so that it has been difficult to synthesize available data for a comprehensive analysis. Here, we combine eight human population-genetic data sets at the 645 microsatellite loci they share in common, accounting for procedural differences in the production of the different data sets, to assemble a single data set containing 5,795 individuals from 267 worldwide populations. We perform a systematic analysis of genetic relatedness, detecting 240 intra-population and 92 inter-population pairs of previously unidentified close relatives and proposing standardized subsets of unrelated individuals for use in future studies. We then augment the human data with a data set of 84 chimpanzees at the 246 loci they share in common with the human samples. Multidimensional scaling and neighbor-joining analyses of these data sets offer new insights into the structure of human populations and enable a comparison of genetic variation patterns in chimpanzees with those in humans. Our combined data sets are the largest of their kind reported to date and provide a resource for use in human population-genetic studies.

June 11, 2013

My own opinions on this matter have been repeated ad nauseam in this blog, so I will only briefly touch on a couple of points in this new article.

Contrary to the authors' claim that: "The size of the mtDNA database is very substantial: currently there are almost 13,000 complete non-African mtDNA genomes available, not one of which is pre-L3." there are plenty of pre-L3 mtDNA in Eurasia. Some (or indeed most?) of these might represent more recent African admixture, and one could argue why they believe that to be the case, but no one has ever studied pre-L3 Eurasian mtDNA to conclude that none of it had an ancient presence in Eurasia. The native non-existence of pre-L3 in Eurasia is a viewpoint, not a fact.

Second, the authors present the following table:

Note, however, that they have chosen to date the common ancestor of all African sublineages (to ~70.2ky using ML method), but they have not done the same for the common ancestor of all non-African sublineages (i.e., M+N). A recent study estimates M+N to be 77KBP and L3 to be 78.3KBP, with other possibilities depending on method and portion of the molecule examined.

At present, I see no good reason to think that haplogroup L3 originated either in Africa or Eurasia; one could argue for an African origin, but temporal priority for African L3 is not established. The only thing that seems to be established is that there are "more" L3 subclades in Africa, which is phylogenetically meaningless until the bifurcating structure of the L3 subtree is resolved. And, we should also not forget that the Toba eruption did not cause a volcanic winter in Africa, nor was Africa affected by the drying up of the Sahara-Arabia belt c. 70kya, both of which may have suppressed Eurasian mtDNA variation within L3, irrespective of its ultimate origins. And, as I've argued before, both Toba and the post-70kya ecological crisis are excellent candidates for a Eurasian bottleneck caused by pre-existing populations surviving in refugia such as this.

Finally, the authors dismiss the possibility of an overestimated autosomal mutation rate and its implications for human history: "Recent reestimates of the autosomal mutation rate from whole-genome pedigree data suggest a European–Asian split time of 40–80 ka, although they do not, as has been suggested, lend any support to a dispersal fromAfrica before 80 ka (36) (Genetics)."
Actually, the most recent estimate might be consistent with a ~96ky split of Africans from non-Africans, and the mutation rate issue is material to the timing of the African/non-African split. It's not clear where the needle will settle when the issue is resolved, but there's plenty of room for both pre- and post-Toba Out-of-Africa as things stand.

PNAS doi: 10.1073/pnas.1306043110

Genetic and archaeological perspectives on the initial modern human colonization of southern Asia

Paul Mellars et al.

It has been argued recently that the initial dispersal of anatomically modern humans from Africa to southern Asia occurred before the volcanic “supereruption” of the Mount Toba volcano (Sumatra) at ∼74,000 y before present (B.P.)—possibly as early as 120,000 y B.P. We show here that this “pre-Toba” dispersal model is in serious conflict with both the most recent genetic evidence from both Africa and Asia and the archaeological evidence from South Asian sites. We present an alternative model based on a combination of genetic analyses and recent archaeological evidence from South Asia and Africa. These data support a coastally oriented dispersal of modern humans from eastern Africa to southern Asia ∼60–50 thousand years ago (ka). This was associated with distinctively African microlithic and “backed-segment” technologies analogous to the African “Howiesons Poort” and related technologies, together with a range of distinctively “modern” cultural and symbolic features (highly shaped bone tools, personal ornaments, abstract artistic motifs, microblade technology, etc.), similar to those that accompanied the replacement of “archaic” Neanderthal by anatomically modern human populations in other regions of western Eurasia at a broadly similar date.

All of the samples studied have a different sequence of mitochondrial DNA HVR I (Table). An analysis of haplotype structure enabled its attribution to five mitochondrial DNA haplogroups: western Eurasian U2e, U5a, T and eastern Eurasian C and A10. A mixed gene pool structure combining mitochondrial DNA groups typical of human populations from western and eastern parts of Eurasia, have been ascertained for all ancient Western-Siberian forest-steppe human populations that we have studied to date (Pilipenko, 2010).

The authors identify two components in the population: (i) the "indigenous" mixed population of West Eurasian (U2e+U5a) and East Eurasian (A10+C), and (ii) the intrusive Andronovo (Fedorovka) (T). They also hint about a special article on the autochthony of the A10 lineages in the region. We now seem to have fairly good data about the existence of a wide West/East Eurasian interaction zone from eastern Europe to Siberia, and it would certainly be interesting to see when this zone was first formed; in any case, it seems clear that at least in the central-northern parts of Eurasia admixture between East and West has been going on for a while.

The more interesting question is where did the mtDNA haplogroup-T in Fedorovo groups come from? In Europe, for which we have the best data, T makes its appearance with early Neolithic groups, but it's difficult to imagine that this was the source of T in West Siberia. I would not be surprised if the entrance of T into the boreal zone occurred via the Caucasus, although Grigoriev derives them "from the Near East through Iran and Central Asia into the Irtish basin." Ancient DNA reveals the gradual appearance of new players in both Europe and West Siberia, but their ultimate source(s) and migratory paths remains elusive.

An Analysis Of Mitochondrial Dna From The Pakhomovskaya Population Of The Late Bronze Age, Western Siberia

V.I. Molodin et al.

This article presents the results of an analysis of mitochondrial DNA extracted from bone samples from Stary Sad – a burial ground representing the eastern variant of the Late Bronze Age Pakhomovskaya culture in the Baraba forest-steppe, Western Siberia. Comparison with mitochondrial DNA data from earlier populations of the region and also with archaeological facts, points to the origins of the Pakhomovskaya people. Certain components of their gene pool were evidently derived from the local pre-Andronovo populations, others from the actual Andronovo (Fedorovka) population and also from later immigrants. In this article an integrative reconstruction based on biological and cultural facts is proposed.

June 08, 2013

genetiker calls me "dumber than he thought" and responds to my criticism of his model. As always, I will disregard the name calling and deal with the (much more interesting) facts.

First, he writes:

In his post Dienekes takes the phylogeny I used for running the F4 ratio estimation program and shows that it won’t work for f3 statistics.

No kidding.

No kidding indeed. Either genetiker believes in his phylogeny or he doesn't. The fact that the F4 ratio estimation program requires a phylogeny with that structure is meaningless: as I have shown, that phylogeny is wrong because it makes a prediction that is falsified by the data. Garbage in-garbage out, so the estimates obtained by genetiker with the wrong phylogeny are of course... wrong.

Second, he presents an even more elaborate phylogeny, where "V is Veddoids, C is Caucasoids, M is Mediterraneans, N is Nordics, G is Mongoloids, S is Sardinians, E is Europeans, and A is Amerindians."

This phylogeny is of course also wrong, for at least two reasons:

It ignores post-admixture drift in Europeans, i.e., the drift that has accumulated after E was formed by M+N. This drift is always traversed in the same direction from E to S and to A, so it contributes a constant positive term in the value of F3(E; S,A)

It proposes instantaneous formation of S, E, and A, e.g., the "Nordic" component in Europeans is symmetrically related to the "Nordic" component in Sardinians and Amerindians. genetiker clearly does not believe this, since he argues in his site (i) for I-M26 bearing "White Gods" coming to the Americas via the Canary islands, (ii) that mtDNA haplogroup X in the Americas is Caucasoid and so is (iii) Y-haplogroup C, which although "originally Veddoid" was carried by "Caucasoids" into the Americas. Now there's zero evidence that any of this has anything to do with Caucasoids, let alone Nordics in the Americas, but in any case it would be nice if genetiker harmonized his convoluted model of "Nordic" migrations with his phylogeny. In other words, his mental model of what happened isn't only inconsistent with the data, it's also inconsistent with itself.

Finally, genetiker attempts to work out the mathematical details of his model, arriving at the conclusion that:

There are four paths from Europeans to Sardinians and four paths from Europeans to Amerindians, so there are sixteen path combinations.

This is of course wrong, because these paths are not independent; one actually needs to sum over 8 (=2^3) different trees for the different combinations of α, β and γ in the model; genetiker is therefore using wrong math applied to a wrong model. I believe his confusion stems from conflating admixture edges with drift edges.

It is not clear what he has aimed to accomplish with this "model", but let's analyze it properly:

If α,β or 1-α,1-β then because of the instantaneous derivation of S,E from M and N respectively there is no drift in the degenerated length-0 "path" E-to-S, and hence F3(E; S,A) = 0. So, we only have to consider the cases α, 1-β and 1-α, β:

If 1-γ then if α,1-β we have drift overlap MC, or if β,1-α we have drift overlap CN

If γ then then if α,1-β we have drift overlap MC+CN, or if β,1-α we have drift overlap 0

So, in total we have a positive F3(E; S, A) statistic again, since we are summing over positive or zero drifts. If we also added the post-admixture drift in E, that statistic would be even higher -although this is not really necessary to falsify genetiker's model.

In any case, I still applaud genetiker for engaging with the data, and I'm happy to contribute to his continuing education!

June 07, 2013

An interesting new paper has appeared in PLoS Genetics, with what appears to be a nice new method for inferring demographic history from genome-scale data. The authors observe that segments inherited from common ancestors are "broken up" by mutation as time goes by: initially there are long identical tracts, but these are "split" whenever a new mutation appears, so they study the distribution of lengths of the pieces between mutations that remain identical by state.

A practical application of the new technique is applied to European-African history:

We estimate that the European-African divergence occurred 55 kya and that gene flow continued until 13 kya. About 5.8% of European genetic material is derived from a ghost population that diverged 420 kya from the ancestors of modern humans. The out-of-Africa bottleneck period, where the European effective population size is only 1,530, lasts until 5.9 kya.

The authors use the "old" 2.5x10-8 mutation derived from a paleontological calibration of the human-chimp split, which renders their calculations comparable to many past papers on human demographic history, but at odds with many of the newer rates that are approximately twice slower. There is lingering controversy about the appropriateness of different rates.

The authors estimate that perhaps a 1.75x increase in their estimates will be effected if the slower rates are used; this is not 2x as one might expect from a 2x slower rate, because their age estimates depend on both the mutation rate (for which there is controversy) and the recombination rate. By applying the 1.75x correction factor, we may obtain a time for European-African split at 96 thousand years and a continuation of gene flow between Europeans and Africans down to 23 thousand years.

I suppose that things might be complicated by the occurrence of Amerindian-like admixture in some West Eurasians in the past, as well as the occurrence of intra-African admixture (which I've called "Palaeoafrican") in the ancestry of Yoruba, both of which do not appear to be modeled here: the former might have infused an "African-less" component of ancestry at a time when the authors suggest that there was continuing gene flow between West Eurasia and African; the latter would inflate the effective population size of the Yoruba and make the appear earlier diverged from non-Africans.

In any case, this is a useful addition to our understanding of human history and may tie in to some of my arguments about Eurasian back-migration into Africa (although the authors consider bidrectional gene flow in their model). The lack of non-M,N mitochondria in non-Africans makes the post-OoA gene flow from Africa->Eurasia difficult to stomach, while the opposing migration of Y-haplogroup E bearers into Africa (as I have suggested) seems too instantaneous to account for the authors' evidence for protracted gene flow.

PLoS Genet 9(6): e1003521. doi:10.1371/journal.pgen.1003521

Inferring Demographic History from a Spectrum of Shared Haplotype Lengths

Kelley Harris, Rasmus Nielsen

There has been much recent excitement about the use of genetics to elucidate ancestral history and demography. Whole genome data from humans and other species are revealing complex stories of divergence and admixture that were left undiscovered by previous smaller data sets. A central challenge is to estimate the timing of past admixture and divergence events, for example the time at which Neanderthals exchanged genetic material with humans and the time at which modern humans left Africa. Here, we present a method for using sequence data to jointly estimate the timing and magnitude of past admixture events, along with population divergence times and changes in effective population size. We infer demography from a collection of pairwise sequence alignments by summarizing their length distribution of tracts of identity by state (IBS) and maximizing an analytic composite likelihood derived from a Markovian coalescent approximation. Recent gene flow between populations leaves behind long tracts of identity by descent (IBD), and these tracts give our method power by influencing the distribution of shared IBS tracts. In simulated data, we accurately infer the timing and strength of admixture events, population size changes, and divergence times over a variety of ancient and recent time scales. Using the same technique, we analyze deeply sequenced trio parents from the 1000 Genomes project. The data show evidence of extensive gene flow between Africa and Europe after the time of divergence as well as substructure and gene flow among ancestral hominids. In particular, we infer that recent African-European gene flow and ancient ghost admixture into Europe are both necessary to explain the spectrum of IBS sharing in the trios, rejecting simpler models that contain less population structure.

June 06, 2013

The placement of Caribbeans on a European "genetic map" is fairly interesting, as they appear to be "ultra-Iberian" (on the far left). The authors invoke drift as an explanation, which makes sense, given that a small portion of the Iberian gene pool entered into the composition of these populations.

On the other hand, it'd be nice to have Iberian data from a few centuries ago, to make sure, since Iberia, being a part of Europe may have had the opportunity to "right-shift" during the last few centuries due to gene flow, and even if it didn't there is a chance that gene flow within Iberia may have dulled population differentiation, while immigration to the Caribbean may not have originated from all parts of Iberia equally (and as I've shown, there is substantial population structure in Iberia down to this day).

arXiv:1306.0558 [q-bio.PE]

Reconstructing the Population Genetic History of the Caribbean

Andres Moreno-Estrada et al.

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, by making use of genome-wide SNP array data, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups. We provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. The Caribbean-derived European component shows significant differentiation from parental Iberian populations, presumably as a result of founder effects during the colonization of the New World. Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures in present day Afro-Caribbean genomes and shedding light on the genetic impact of the dynamics occurring during the slave trade in the Caribbean.

A nice overview paper comparing various methods used in population genetics has appeared on the arXiv.

arXiv:1306.0701 [q-bio.PE]

Populations in statistical genetic modelling and inference

Daniel John Lawson

What is a population? This review considers how a population may be defined in terms of understanding the structure of the underlying genetics of the individuals involved. The main approach is to consider statistically identifiable groups of randomly mating individuals, which is well defined in theory for any type of (sexual) organism. We discuss generative models using drift, admixture and spatial structure, and the ancestral recombination graph. These are contrasted with statistical models for inference, principle component analysis and other `non-parametric' methods. The relationships between these approaches are explored with both simulated and real-data examples. The state-of-the-art practical software tools are discussed and contrasted. We conclude that populations are a useful theoretical construct that can be well defined in theory and often approximately exist in practice.

June 05, 2013

genetiker, a new genome blogger questions the existence of Amerindian-like admixture in Europe. I am generally well-disposed to anyone who tries their hand at analysis of genetic data. On the other hand, if one accuses me of writing a series of posts "chock-full of stupidity", then there's a good chance I might respond. This should also be useful for anyone wishing to understand the evidence for this admixture.

genetiker proposes that the "Amerindian-like" admixture in North Europeans is misunderstood and can be in fact explained by the existence of "North European-like" admixture in Amerindians. In support of this, he presents the results of an F4 Ratio estimation analysis which suggests that there is "Nordic admixture of the Amerindian populations in the 10 to 20 percent range."
F4 Ratio estimation produces admixture estimatesbut does not prove the existence of such admixture. The admixture estimates are as good as the relationship proposed for a particular set of populations. If the relationship is nonsensical, so will be the admixture estimates.

According to genetiker, the following relationship holds, with A=Sardinian, B=Orcadian, C=Dai, and O=Yoruba, with X=Amerindians.

But, is the above consistent with the data? The existence of Amerindian-like admixture was argued by Patterson et al. (2012) on the basis of the following F3 statistic (right):

F3(European; Sardinian, Amerindian)

which is signifantly negative for North Europeans. Now, consider the value of this statistic for genetiker's phylogeny.

F3(B = North European; A = Sardinian, X = Amerindian)

In the above figure I color-coded the path from B=North European to A=Sardinian (red) and from B=North European to X=Karitiana (green, if it goes via the supposed "North European" admixture, or blue, if it goes via the "Amerindian" admixture). The value of the F3 statistic is then the weighted sum of the overlap of the red/green and red/blue paths:

F3(B; A, X) = αBZ+(1-α)(BZ+ZW)

where BZ and ZW are drifts along the paths indicated in the figure. This statistic is then always positive, since the common segments in the graph are traversed in the same direction.

genetiker's model is thus falsified by the data: it predicts a positive f3(North European; Sardinian, Amerindian) statistic, but we in fact observe negative ones.

June 04, 2013

I had posted a few studies suggesting links between Mycenaean Greece and Scandinavia, and here is another one. From the paper, this ties a bit to my ideas about the establishment of long-range networks associated with metallurgy in the Bronze Age:

It can be seen that there were two, chronologically separate, lines of introduction or transfer of the razor idea from the eastern Mediterranean to northern Europe. The spread of the two-edged razor to Central and Western Europe including Britain and Ireland took place just before or around 1500 BC. The one-edged razor arrived in Scandinavia in the decades before 1400 BC. The two ‘time-slots’ of transfer from the Mediterranean of two types of razors indicate the use of specific long distance networks that were probably in existence beforehand.

The bronze razor with the horse-head handle appeared in Scandinavia in the fifteenth century BC. Where did it come from and what did it mean? The author shows that the razor had some antecedents in the Aegean, although none of these objects were imported to the north. He argues that the Scandinavian warrior class consciously adopted elements of the Mycenaean warrior package, including a clean-shaven face. This vividly exposes new aspects of the busy and subtle nature of international communication in the Bronze Age.

An interesting new paper documents an excess of IBD sharing between Iberians (excluding Basques) and North African (and particular NW African) populations.

It would have been nice if the authors had used techniques such as rolloff and ALDER or those of Jin et al. (2012) to say something about the time/nature of the admixture event detected via IBD sharing; insteady, they use variance in admixture proportions, which gives a probably much noisier estimate, with the basic idea being that in the first few generations post-admixture there are individuals with much varying admixture proportions, but these tend to be homogenized over time.

The occurrence of North African-specific admixture in SW Europe has long been suspected on the basis of Y-chromosome/mtDNA work (e.g., the presence of E-M81 which is probably the best North African marker in existence). It also makes sense, because of the limited occurrence of Sub-Saharan markers in Iberia: such elements did not, presumably, fly over North Africa, but landed in Iberia via people who were themselves admixed.

A couple notes of caution:

(i) the use of ADMIXTURE as a means of estimating admixture proportions is dangerous in this case, because of the hybridity of "North Africans" themselves, which according to published estimates experienced Sub-Saharan African admixture in the last few thousand years. In my own experiments it is clear that "North Africans" are a mixture of three basic components related to Europe, Sub-Saharan Africa, and the Near East. Nonetheless, in my own experiments I do also get an excess of the component I've labeled "Northwest African" in Iberia that is not shared by Basques or French.

(ii) as I've emphasized before, IBD sharing between populations does not indicate the direction of gene flow. One would have to look at the ancestry of the shared segments to determine their origin. To give a simple example, an IBD segment shared by a Spaniard and a Mexican could be European, African, or Native American, and -thanks to historical knowledge- we can be fairly sure that the number of such segments is also in the given order.

Given that Iberia is the neighbor of NW Africa one would not be surprised if there was gene flow in both directions, and while North Africa gene flow into Iberia is one possible explanation, some of the gene flow may have gone the other way, e.g., with contacts during the Pax Romana, fleeing Iberian Muslim in the post-reconquista period, Barbary pirates attacking Christian ships and the like. In any case, it would be interesting to catalogue IBD shared segments between Iberia and NW Africa in terms of their geographical origin.

(iii) the sources and timing of admixture could potentially be determined by ancient DNA work. The three most recent time periods are related to the slave trade (both European of Africans and vice versa), the Islamic period, and the Roman Empire. Presumably, with the sampling of enough individuals, that type of admixture ought to manifest in populations living before/after each of these three events.

In any case, this is an interesting paper which is also accompanied by publicly accessible data.

Human genetic diversity in southern Europe is higher than in other regions of the continent. This difference has been attributed to postglacial expansions, the demic diffusion of agriculture from the Near East, and gene flow from Africa. Using SNP data from 2,099 individuals in 43 populations, we show that estimates of recent shared ancestry between Europe and Africa are substantially increased when gene flow from North Africans, rather than Sub-Saharan Africans, is considered. The gradient of North African ancestry accounts for previous observations of low levels of sharing with Sub-Saharan Africa and is independent of recent gene flow from the Near East. The source of genetic diversity in southern Europe has important biomedical implications; we find that most disease risk alleles from genome-wide association studies follow expected patterns of divergence between Europe and North Africa, with the principal exception of multiple sclerosis.

The Himalayan mountain range is strategically located at the crossroads of the major cultural centers in Asia, the Middle East and Europe. Although previous Y-chromosome studies indicate that the Himalayas served as a natural barrier for gene flow from the south to the Tibetan plateau, this region is believed to have played an important role as a corridor for human migrations between East and West Eurasia along the ancient Silk Road. To evaluate the effects of the Himalayan mountain range in shaping the maternal lineages of populations residing on either side of the cordillera, we analyzed mitochondrial DNA variation in 344 samples from three Nepalese collections (Newar, Kathmandu and Tamang) and a general population of Tibet. Our results revealed a predominantly East Asian-specific component in Tibet and Tamang, whereas Newar and Kathmandu are both characterized by a combination of East and South Central Asian lineages. Interestingly, Newar and Kathmandu harbor several deep-rooted Indian lineages, including M2, R5, and U2, whose coalescent times from this study (U2, >40 kya) and previous reports (M2 and R5, >50 kya) suggest that Nepal was inhabited during the initial peopling of South Central Asia. Comparisons with our previous Y-chromosome data indicate sex-biased migrations in Tamang and a founder effect and/or genetic drift in Tamang and Newar. Altogether, our results confirm that while the Himalayas acted as a geographic barrier for human movement from the Indian subcontinent to the Tibetan highland, it also served as a conduit for gene flow between Central and East Asia.

This paper casts doubt on the dominant scenario about the Southeast Asian geographical origin of dogs, while at the same time affirming their monophyletic origin and late pre-Neolithic domestication. The authors also document traits that were under selection during domestication.

It would be interesting to know what kinds of roles early dogs. Presumably early pre-Neolithic dogs functioned more as hunting companions, while those of Neolithic societies also had an increasing role as guards -since there was then property that needed guarding. How do modern dog breeds differ genetically to accommodate these roles, and might we one day figure out the original tasks of "multi-purpose" animals such as dogs?

arXiv:1305.7390 [q-bio.GN]

Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs

Adam H. Freedman et al.

To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we analyzed novel high-quality genome sequences of three gray wolves, one from each of three putative centers of dog domestication, two ancient dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. We find dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow, which confounds previous inferences of dog origins. In dogs, the domestication bottleneck was severe involving a 17 to 49-fold reduction in population size, a much stronger bottleneck than estimated previously from less intensive sequencing efforts. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was far larger than represented by modern wolf populations. Conditional on mutation rate, we narrow the plausible range for the date of initial dog domestication to an interval from 11 to 16 thousand years ago. This period predates the rise of agriculture, implying that the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that surprisingly, none of the extant wolf lineages from putative domestication centers are more closely related to dogs, and the sampled wolves instead form a sister monophyletic clade. This result, in combination with our finding of dog-wolf admixture during the process of domestication, suggests a re-evaluation of past hypotheses of dog origin is necessary. Finally, we also detect signatures of selection, including evidence for selection on genes implicated in morphology, metabolism, and neural development. Uniquely, we find support for selective sweeps at regulatory sites suggesting gene regulatory changes played a critical role in dog domestication.

A useful review paper that should be useful to anyone trying to understand the broad patterns of Asian prehistory.

Investigative Genetics 2013, 4:11 doi:10.1186/2041-2223-4-11

Inferring human history in East Asia from Y chromosomes

Chuan-Chao Wang and Hui Li

Abstract (provisional)

East Asia harbors substantial genetic, physical, cultural and linguistic diversity, but the detailed structures and interrelationships of those aspects remain enigmatic. This question has begun to be addressed by a rapid accumulation of molecular anthropological studies of the populations in and around East Asia, especially by Y chromosome studies. The current Y chromosome evidence suggests multiple early migrations of modern humans from Africa via Southeast Asia to East Asia. After the initial settlements, the northward migrations during the Paleolithic Age shaped the genetic structure in East Asia. Subsequently, recent admixtures between Central Asian immigrants and northern East Asians enlarged the genetic divergence between southern and northern East Asia populations. Cultural practices, such as languages, agriculture, military affairs and social prestige, also have impacts on the genetic patterns in East Asia. Furthermore, application of Y chromosome analyses in the family genealogy studies offers successful showcases of the utility of genetics in studying the ancient history.

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